Figure 1

Reverse transcriptase sequences found in the genome of Drosophila melanogaster. Phylogenetic trees of sequences matching the full-length hidden Markov model of reverse transcriptase as defined by HMMER 2.1.1 that were identified in the analysis of (a) Release 1 and (b) BDGP/EDGP sequences. Names on branches represent GenBank accession numbers followed by coordinates in the respective sequence, which confine the HMM match (start coordinate greater than end means reverse complement of a sequence). Distinct families are separated by clades according to [2]. The tree was constructed by the neighbor-joining method as implemented in CLUSTAL W software. Numbers at the nodes represent bootstrap values as percentages out of 500 replicates and are shown only for values greater than 50%. Because of redundancy present in the BDGP/EDGP data set, absolutely identical sequences were substituted by one representative each in building the tree in (b).